## Monday, November 17, 2008

### Inline PDF viewing with Firefox on OS X

For OS X/Firefox users, you can use this PDFkit Plugin for Firefox
for inline PDF viewing, if you are not happy with other options:
Schuber|it PDF Plugin

Mitch Keeler writes about 6 PDF tools for Firefox.
If you are not an OS X, you can troubleshoot the Adobe plugin.

## Wednesday, January 2, 2008

A friend sent a link to a YouTube video saying the theory of evolution is dead. These are all about the same, and usually rehash each other's arguments, rather than fresh ones. anyone who says that scientific data has destroyed the theory of evolution is either an idiot or hoping the audience are idiots; there is no third option. there is no such collapse of evolution. most people (when i say most, i mean everyone i have seen thus far) who has a problem with the current model of evolution have demonstrated that they do not understand how it works: the time scales involved, mechanisms of single point substitutions, recombination, gene cassettes, endogenous retroviruses, etc. all of these together can do very powerful things to the genome of an organism.

my main problem with ID is the completely adolescent, illogical philosophy of it: the origins of life are far too complicated to explain, so to explain them, we believe that something even more complicated created it. this immediately fails Ockham's Razor.

evolution is not complete, but it is still the best explanation given all the evidence. and filling in the unknowns with God is absurd. just because we don't know (yet) is a silly reason to ascribe the phenomenon to some space pixie (especially a pixie as described by Judeo-Christian mythology, myths that are contradictory, asinine, etc.) If there is a god-like being(s), it bears no resemblance to our concept of God. such beliefs, to me, are childish and pathetic, the height of delusion. people are afraid of life, its dangerous, so they fabricate this bullshit to comfort themselves. when i argue with Christians about their mythology (eg we can stone someone to death for working on the Sabbath), i almost always get them to admit that they believe because to not believe is too scary/depressing. that is the very definition of delusion.

there is no evidence to support this. none. any supposed evidence is just bad logic or pseudoscience masquerading as evidence. for a mind-numbing experience, dig into the blogosphere on this:

Two good places to start:
http://www.pandasthumb.org/
http://endogenousretrovirus.blogspot.com/

Google for Michael Behe, professor at Lehigh in PA, a leading proponent of ID:

most of his arguments do not stand up to rigorous scientific or logical examination, but he is the flipside, pro-ID voice. do some reading, evaluate the evidence, there will be a quiz.

## Wednesday, December 12, 2007

### Denialism's roots

There are many groups of denialists out there, but i am mostly concerned today with those that deny HIV causes AIDS. Its a bit of a bait and switch: they start by trying to sound reasonable -- "are we SURE HIV causes AIDS?", and then, contending that we are in fact not SURE, move straight to HIV does NOT cause AIDS.

But what i really find laughable is one of the cornerstones of the theory, i.e. a vast conspiracy by a medical industrial complex that stifles dissent in favor of billions of dollars of profits poured into research that is doomed to fail, mostly because it targets the wrong virus. The fallacious assumptions here are numerous, but to sum up briefly:
1. Scientists are generally not well paid compared to other professions with similar levels of training (i, for instance, have been working in biochemistry for 17 years and make 40K/year with a Ph.D.). People in the biological sciences are noted for having one the highest levels of training with the lowest salaries, on average. In a way, we are not very bright, eh? Scientists do not profit personally from any research grants. When we are awarded a research grant, it means we can continue to work, studying either a biological phenomenon or disease because we enjoy studying things, finding cures for things, etc. When the grants are not funded, like when your defense budget + "emergency spending" is the better part of $1,000,000,000,000, then we lose our jobs and wind up working at Starbucks (at my level anyway, but i am a lowly post doc), and no one has a better understanding anything. 2. Scientists thrive on argument. It is what we are trained to do. i don't mean argument in the "you suck", "no, YOU suck" way, but more like "i think its like this, based on my results", "yeah, well, your results are obviously flawed, and it is actually like this, based on my results", and on and on in the peer-reviewed literature, the peers being other scientists who may have their own theories based on their results, or may believe the results of someone else. Peruse the literature of any single field in the biological sciences, and you will find discord and disagreement. Mechanisms of oncogenesis, cell signaling, should you include all of your diffraction data or stop at some arbitrary signal to noise ratio. Debate, it is the nature of science. To think that all these academic scientists would quietly go along with some HIV conspiracy so that some multinational corporation can make billions is flawed in the extreme. Scientists will form a consensus when every other explanation for a particular phenomenon makes less sense than the favored explanation. Evolution, for instance. You may posit alternate theories if you wish, but nothing else agrees with the observations as well as evolution, and so is accepted as the most plausible explanation speciation. 3. If the purpose of the multinational Big Pharma is to milk the HIV crisis for all its worth, why are they giving loads of antiretroviral therapy cocktails to Africa and Asia for pennies on the dollar, free in some cases? Go to all this trouble to set up this well crafted conspiracy to make billions, only to donate money to the hardest-hit nations. To wit, Highly Active Antiretroviral Therapy (HAART) in the US is$12-15000/yr/patient. In Thailand, it is $400/yr/patient, and in many regions in Africa, it is$0/yr/patient. If one wanted to make as much money as possible, this seems counterproductive to me.
So what do i think is happening? I am not really sure. A lot of the "dissidents" are lay people, so their opinion may be ill informed, maybe not. I don't know them. But some are scientists. Perhaps they are people of note, or at one time were of note, and they miss being "of note", and crave ways to get some attention again for having great ideas. A great idea, almost by definition, must be one not shared by many other people, otherwise it is merely conventional wisdom. Boring. A further observation: the work of many scientists into HIV plays out in the aforementioned peer-reviewed literature, much of which is available free online. Look here. If the papers are not available to you, try to access the website from a library. They sometimes pay the subscription fees for the online journals that are not made freely available. Or buddy up with someone at a research university, and talk to them about the literature. Start a journal club, where you can discuss the merits or problems of specific papers. Scientists do this all the time. It is critical to try to objectively evaluate the current literature: what is good, and what is sloppy, etc.

In contrast, just about all of the dissident literature, mostly books, must be purchased. It is not made freely available, nor is it possible to have a critical dialogue. Publishing a book is a bit of a bully pulpit. The avenues for rebuttal are not as accessible. "I know what they don't want you to know. I explain all in my book, avaliable here for \$19.99. Buy Today! Before its too late!" Some movies have popped up on YouTube, but these are honestly so illogical as to approach painful, and may be unauthorized uploads anyway. So, it seems to me that the people profiting the most personally from the HIV/AIDS debate are the dissidents who decry the existence of this vast conspiracy. Ironic, no? Or evil genius, depending on how you look at it. Basically, i am saying that the dissidents are either not thinking critically or are actually preying upon FUD for profit.

## Wednesday, November 7, 2007

### An Introduction

Howdy! Bore da! this blog will serve as a repository for things i find interesting. These areas will include, but likely not be limited to, structural biology, virology, LaTeX geekery, computational biology, etc. It may also include thoughts on philosophy, (a)theism, and rantings about the Nobel Prize (it's a tawdry beauty pageant!).

### Cross-referencing in LaTeX

So far, my attempts to incorporate cross references in LaTeX documents is adequate, but it seems possible to include wiki-esque usage of links within the PDF output. Thus far, attractive packages include:

• xr - for Xternal References to other documents (part of the required tools package)
• smartref - modifies the behavior of hyperref, improving refences across chapters
• hypcap - relocate the caption anchor to the top of the "float" (part of the Oberdiek bundle)
Incorporating these into the style file improves references over the vanilla \ref and \href commands. Also, creating footnotes of the hyperlink may improve forwards readability should the links go off.